SpotSpace: Methods for Projecting Network Signals in Spatial Transcriptomics

The SpotSpace package extends PathwaySpace methods alongside Seurat workflows, providing tools for signal propagation and visualization in spatial transcriptomics. By integrating signal processing with spatial visualization, SpotSpace allows users to project network signals onto spot-level coordinates to explore signal patterns on tissue microenvironments.

Installation in R (>=4.4)

Dependencies to build the vignettes

install.packages("knitr")
install.packages("rmarkdown")
install.packages("remotes")

Development version

# Main packages
remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)
remotes::install_github("sysbiolab/PathwaySpace", build_vignettes=TRUE)
remotes::install_github("sysbiolab/SpotSpace", build_vignettes=TRUE)

# Data package used in the examples
remotes::install_github("satijalab/seurat-data")

Examples

Follow the SpotSpace vignette and try to make some plots!

library(SpotSpace)
vignette("SpotSpace")

Citation

If you use SpotSpace, please cite:

• Tercan & Apolonio et al. Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods. STAR Protocols, 2025. https://doi.org/10.1016/j.xpro.2025.103681

Licenses

The SpotSpace package is distributed under Artistic-2.0